This script is the data visualization script that: 1) Makes QAQC file of all Secchi data from a digitized google sheet 2) Checks to make sure there are no duplicate in the file 3) Makes sure the maintenance log is working 4) generates figures to visualize both this past year and all combined years of data 5) Save the final EDI file 6) Downloads the qaqc function and the maintenance log for publication
REVIEWERS- If you are reviewing this data package replace the pasta link with the one from EDI. If there are questions ask the data point person.
This section identifies if there are any duplicates. If there are duplicates. Look to see if they are true duplicates and then check the qaqc function to see how they were missed.
| Reservoir | Site | DateTime | Secchi_m |
|---|
Let’s look at the flag Frequency for each variable. As a reminder here are the flag codes
Flag values for DateTime
0: no flag
1: Time set to 12:00:00 because an exact time was not recorded
Flag values for Secchi_m
0: no flag
1: value missing or removed and set to NA
2: multiple observations at a site at the same time are averaged together
3: value changed through the maintenance log
## [1] "Flag_DateTime"
## Flag_DateTime
## 0 1 <NA>
## 573 181 0
## [1] "Flag_Secchi_m"
## Flag_Secchi_m
## 0 2 <NA>
## 750 4 0
We want to make sure that our maintenance log actually worked and took out the values or changes those it was supposed to
| Reservoir | Site | DataStream | TIMESTAMP_start | TIMESTAMP_end | start_parameter | end_parameter | flag | update_value | notes |
|---|---|---|---|---|---|---|---|---|---|
| BVR | 50 | Secchi | 2014-04-30 11:50:00 | 2014-04-30 12:10:00 | Secchi_m | NA | 2 | NA | Averaged observations from the same site at the same time |
| BVR | 50 | Secchi | 2014-07-23 11:50:00 | 2014-07-23 12:10:00 | Secchi_m | NA | 2 | NA | Averaged observations from the same site at the same time |
| FCR | 50 | Secchi | 2014-10-04 11:50:00 | 2014-10-04 12:10:00 | Secchi_m | NA | 2 | NA | Averaged observations from the same site at the same time |
| CCR | 50 | Secchi | 2021-08-19 12:15:00 | 2021-08-19 12:20:00 | Secchi_m | NA | 2 | NA | Averaged observations from the same site at the same time |
Look at the first few rows of the data frame and check that the observations after the TIMESTAMP_start are flagged
| DateTime | Secchi_m | Flag_Secchi_m |
|---|---|---|
| 2021-08-19 12:18:00 | 2.35 | 2 |
Make sure the observations are flagged
## Warning: Removed 31 rows containing non-finite outside the scale range
## (`stat_summary()`).
## Warning: Removed 31 rows containing missing values or values outside the scale range
## (`geom_point()`).
## Warning: Removed 26 rows containing missing values or values outside the scale range
## (`geom_point()`).
# convert DateTime to character
current_df$DateTime <- as.character(format(current_df$DateTime))
write_csv(current_df, 'secchi_depth_2013_2023.csv')
#list.files()